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52 Cards in this Set
- Front
- Back
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Nucleoside
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Nitrogen-containing base
5-carbon sugar ring |
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Nucleotide
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Nitrogen-Containing base
5-carbon Sugar ring Phosphate group |
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Central Dogma
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the idea that once protein is made, it doesn't go back to either RNA or DNA.
Proves replication, transcription, and translation. |
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Purine
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Adenine and Guanine
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Pyrimidines
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Cytosine, Thymine, Uracil
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nucleotides are linked/read
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5' to 3' by a single phosphate group (a phosphodiester bond)
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Base composition is _________ within species
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invariant
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Base composition ____ among species
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varies
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DNA can be single stranded or double stranded. depending on ______ and ______
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Temp, and ionic strength
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Palindrome
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reads same way backwards and forwards when read 5 to 3 on two different strands
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mirror repeat
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reads same way when read 5 to 3 and 3 to 5 on same strand
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Depurination
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removal of purine from DNA with addition of H2O
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Deamination
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removal of amino group. Cytosine to Uracil. 3 to 2 hydrogen bonds... less stable
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UV cross-linking
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Two adjacent thymines form kink in DNA
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Alkaline Base Hydrolysis in RNA
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RNA is cleaved in half. RNA is unstable
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L=
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T + W
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30 nm fibers
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nucleosomes pack DNA to larger fibers. 100 fold compaction. 6 fold symmetry
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DNA is neither ____ nor ____
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uniform nor static
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2 methods of DNA sequencing
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Maxam-Gilbert: uses base-specific chemical methylation to cleave DNA chain at specific bases.
Sanger: enzymatic Uses enzymes and dideoxynucleotides to terminate growing chain at specific bases |
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DNA synthesis in vivo
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3' OH attacks alpha phosphate of nucleotide
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Dideoxynucleotide DNA sequencin in vitro
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no 3' OH to attack phosphate group. no DNA synthesis.
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Oligodeoxynucleotide synthesis in vitro
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Uses modified nucleotides with reactive roups chemically protected. builds oligo 3 to 5 prime.
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Blotting
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detection of specific nucleotides. involves hybridization of probe and washing, and detection
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Southern Blot
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Take chromosomal DNA, cleave with restriction endonuclease, separate fragments by agarose gel.
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Northern Blot
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For RNA. Can see changes in gene expression. Location, time, response.
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Restriction Enzymes
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Allow bacteria to destroy foreign DNA. protection from viruses, scavenge genetic material. USE methylation to tell own DNA apart from foreign.
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DNA REPLICATION IS..
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SEMI-CONSERVATIVE and bi-directional
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DNA synthesis is in 5 to 3 prime and uses ____ for energy
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dNTPs
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in DNA synthesis the growing strand is the ______
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primer
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To replicate DNA, we move along __ to __ to synthesize __ to __ prime
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3 to 5. and 5 to 3.
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DNA synthesis requires 3 things
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single stranded template strand of DNA
H-bonded 3' end (primer) dNTPs |
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Origin of Replication has....
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structure that facilitates strand separation:
DNA unwinding element (DUE) Binding sites for DnaA protein (5 9-bp sequences) |
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DUE
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high AT pairs.
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DnaA
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forms helix in presence of ATP which DNA strand wraps around
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DnaA
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binds to DNA at 9bp repeats and forms helix in presence of ATP. This induces positive supercoiling where wraped in helix and negative supercoiling in adjacent area. This causes strand separation at A/T DUE repeats. DnaA recruits DnaC
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DnaC
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in DNA replication:
Loads 2 DnaB hexamers (needs ATP). |
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DnaB (helicase)
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in DNA replication:
DnaB wind out from origin, unwinding DNA . Also binds Primase so it can lay down primer. |
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SSB
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in DNA replication (single stranded binding protein):
binds to linear DNA opened from DnaB to keep open and linear for polymerase. |
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RNA Polymerase (Primase)
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Synthesizes RNA primer in order to start replication. DNA polymerase cannot start from scratch!
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DNA polymerase III Function
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Starts synthesizing from primer layed down by primase (RNA polymerase). in 5 to 3 direction.
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DNA Pol III components
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DnaB helicase
two Core (composed of alpha, epsilon, and omega units, synthesizes lagging and leading strand of DNA) Beta clamp loader (loads on new Beta clamp on Primer, requires ATP) |
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Beta clamp
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forms tight ring around DNA - Allows enzyme to proceed without falling off
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Nick Translation
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Removal of RNA primers and gaps in okazaki fragments via DNA polymerase I and DNA ligase.
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DNA polymerase I
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has 5 to 3 exonuclease activity. chews up RNA primers and lays down new DNA. releases rNTPs and requires dNTPs.
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DNA ligase
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Glues final nick in DNA lagging strand. Requires ATP.
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Telomerase
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extends single stranded end of chromosome to protect from loss. a reverse transcriptase (requires RNA) is a DNA polymerase. Hybridizes to last several bases on end of chromosome, uses end as primer.
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Telomere
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region of repeated short sequence at end of eukaryotic linear chromosome.
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Proofreading during DNA replication
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DNA polymerases have good proofreading 3 to 5' exonuclease activity where they chew off bad base and add new one in that position.
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DNA Repair after replication
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DNA Pol II involved.
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Excision Repair after DNA replication
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UV light damage.
Excinuclease chops out damage DNA helicase unwinds DNA pol I fills gap DNA ligase fills nick |
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How to tell which strand is correct strand to repair??
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methylation identifies parent strand. For a short while the new strand is not methylated until Dam methylase comes in and methylates it then it is no longer possible to tell which strand is parent.
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Mismatch repair
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Requires ATP.
Mismatch cut out by Mut S,L and H. DNA helicase II Exconuclease VII Gap filled by DNA pol III and SSB |
